At the end of this workshop, you will:

Query the Ensembl database via Perl scripts for various types of genomic data

Learn about the Ensembl REST API

Know how to search the API Doxygen documentation

Modules

Dec 2nd: Core Perl-API and the REST API

Alessandro Vullo (Ensembl Core team) will cover basic access to the Ensembl database: how to retrieve basic genome features, such as genes and transcripts, repeat features and sequences, and meta-data about the genomes themselves.

Dec 3rd: Variation Perl-API

Anja Thormann (Ensembl Variation team) will show how to access short (e.g. SNPs, indels) and large scale (e.g. CNVs) variants in the Ensembl database, and how to retrieve information about them, such as location, alleles and population genetics.

Dec 4th: Regulation Perl-API

Thomas Juettemann (Ensembl Regulation team) will cover the different kinds of regulation data (e.g. ENCODE, Roadmap Epigenomics) that Ensembl use in the regulatory build, how this build takes place and how it can be accessed programmatically.

Dec 5th: Compara Perl-API

Matthieu Muffato (Ensembl Compara team) will show how to get gene trees from the Ensembl database, including ncRNA genes and protein alignments. Stephen Fitzgerald (Ensembl Compara team) will then focus on how to access whole genome alignments from the Ensembl database, how to find syntenic regions and conservation scores.

The main pre-requisite is to know how to program in Perl. More details and registration: